Identification and characterization of a novel alpha-amylase from maize endosperm

ABSTRACT

SHE, a Starch Hydrolytic Enzyme active in maize endosperm ( Zea mays ), and the cDNA sequence encoding SHE are disclosed. The specificity of native, purified SHE is similar, in general terms, to previously known alpha-amylases. However, the activity of SHE toward amylopectin results in hydrolysis products that are distinctly different from those of other alpha-amylases. SHE, and its homologous equivalents in other plants such as rice,  Arabidopsis , apple and potato, can be used in starch processing for generating different, e.g., larger sized, alpha-limit dextrins for industrial use, as compared to those generated by previously known alpha-amylases or other starch hydrolytic enzymes. In addition, modification of the expression of this enzyme in transgenic maize plants or in other transgenic organisms (including bacteria, yeast, and other plant species) can be useful for the generation of novel starch forms or altered starch metabolism.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a divisional application of U.S. application Ser. No. 11/891,589 entitled IDENTIFICATION AND CHARACTERIZATION OF A NOVEL ALPHA-AMYLASE FROM MAIZE ENDOSPERM filed Aug. 10, 2007, which claims priority benefit of U.S. application Ser. No. 10/952,551 entitled IDENTIFICATION AND CHARACTERIZATION OF A NOVEL ALPHA-AMYLASE FROM MAIZE ENDOSPERM filed Sep. 27, 2004 and of U.S. Provisional Application No. 60/505,995, filed Sep. 25, 2003, entitled IDENTIFICATION AND CHARACTERIZATION OF A NOVEL ALPHA-AMYLASE FROM MAIZE ENDOSPERM, the whole of which are hereby incorporated by reference herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

N/A

BACKGROUND OF THE INVENTION

Starch is the major storage carbohydrate in higher plants. The biochemical mechanisms of starch biosynthesis and starch utilization are of interest for understanding fundamental aspects of plant physiology and also for their potential utility in manipulating the starch pathway for practical purposes. Not only is starch a critical primary source of dietary carbohydrates, but it is also used extensively for various industrial purposes ranging from formation of packaging materials to ethanol production. Despite its wide availability in nature and its many industrial applications, the mechanisms by which starch is formed and degraded in plant endosperm tissue are not well understood.

Starch consists essentially of a mixture of the homopolysaccharides amylose and amylopectin [11, 24]. Amylose is a linear chain of glucosyl units joined by alpha-1,4 glycosidic bonds and normally constitutes about 25% of the total endosperm starch in maize (Zea mays). Amylopectin comprises many linear chains of glucosyl monomers joined by alpha-1,4 linkages and constitutes approximately 75% of the starch. The chains of amylopectin are joined to each other by alpha-1,6 glycosidic bonds, often referred to as branch linkages. In amylopectin, the organized positioning of branch linkages enables periodic clustering of the linear chains [9, 15]. This permits tight and efficient packaging of glucose units, and confers crystallinity to the granule. The functional properties of starch relate directly to this architectural organization of linear chains and branch linkages in amylopectin [23].

The organization of amylopectin and amylose into higher order structures that lead to granule formation renders starch resistant to degradation. However, starch granules can be completely degraded by a combination of phosphorolysis and hydrolysis when glucose supply is required [2]. As no single enzyme has been shown to completely convert starch to simple sugars, multiple enzymes most likely are involved. Starch debranching enzymes and disproportionating enzymes are potential degradative enzymes, as are the alpha-1,4 linkage-specific hydrolases of the alpha-amylase and beta-amylase classes. Genetic evidence for involvement of an alpha-amylase in starch degradation comes from the sex4 mutant of Arabidopsis, which lacks such an enzyme and accumulates abnormally high levels of starch in leaves [34]. Another enzyme that likely participates in starch degradation is phosphorylase, which inserts phosphoryl groups from inorganic pyrophosphate into the alpha-1,4 glucoside bond, releasing glucose-1-phosphate.

Classification of starch degrading enzymes is made according to their behavior: endo- versus exo- mode of attack, inversion versus retention of anomeric configuration of the substrate, preference for length of the glucosyl chain, preference for the nature of the glucosyl bond, and hydrolytic versus glucosyl-transfer activity [31]. Alpha-amylases are endo-acting hydrolytic enzymes that hydrolyze internal alpha-1,4 linkages in alpha D-glucan polymers, such as amylopectin and amylose molecules. Alpha-amylases are widely distributed in nature, and are produced by plants, animals, and microorganisms [28]. Those from different sources are known to have different substrate specificities, acting preferentially on glucan chains of different lengths. This substrate specificity is dependent on the configuration of the active site of the enzyme and results in characteristic products that are formed according to the enzyme source [28]. For example, salivary gland and pancreatic alpha-amylases immediately produce low molecular weight products such as maltose and maltotriose by “multiple attack” on the substrate [27], and barley alpha-amylase primarily produces maltose, maltohexaose, and maltoheptaose without multiple attack [19]. Because alpha-amylases can hydrolyze linkages only so close to a branch point (generated by an alpha-1,6 linkage), activity halts when this physical limitation occurs. When hydrolytic activity of the alpha-amylase reaches this limit, the resulting product is termed a “limit dextrin”. To achieve further hydrolysis of the limit dextrin, other enzymes must be employed, such as exo-cleaving beta-amylases or debranching enzymes. All of the alpha-amylase activities that have been described to date hydrolyze alpha D-glucans to maltose, maltotriose, or other small malto-oligosaccharides plus alpha-limit dextrins of various sizes [19, 28, 31].

Hydrolysis of starch with alpha-amylases from bacteria or fungi is routinely used by some starch industries as a first step in the process of the complete degradation of starch to glucose (this step is termed “saccharification”). The hydrolysis of starch to glucose is preliminary to the manufacture of conversion products such as high fructose corn syrup or fuel ethanol [18]. The goal of other starch processing industries is the incomplete hydrolysis of starch by various degradative enzymes, including alpha-amylases, to generate limit dextrins (termed “maltodextrins”) in a range of sizes that are used for a variety of industrial purposes. For example, maltodextrins are used in food and pharmaceutical manufacturing as thickening agents, cryoprotectants and binders. They can also be further processed or chemically modified for use as viscosity or hygroscopicity or dissolving agents [13]. Different limit dextrin products are typically produced by varying the combination of enzymes used for the starch digestion, or by varying the digestion conditions. An important industrial goal is the low-energy production of specific starch hydrolysates containing few by-products [18].

In plants, alpha-amylases are believed to be involved in the hydrolysis of transient starch in the leaves, which occurs during the dark cycle of the plant, and in the hydrolysis of storage starch that accumulates in seeds or tubers, which occurs during seed germination or tuber sprouting. The first complete sequence of a plant genome, that of the Arabidopsis genome, reveals that three alpha-amylase genes are present in this plant species [14, 16]. Two are genes that encode predicted polypeptides of approximately 50-60 kilodaltons (kD), and one is a gene that encodes a larger form predicted to have a molecular mass of approximately 100 kD (Genbank Accession No. NM_(—)105651). Sequencing of the rice genome reveals the presence of one homolog of the Arabidopsis gene that encodes the large alpha amylase [12]. This rice gene is also predicted to encode a polypeptide of approximately 100 kD (Genbank Accession No. AP003408). In addition, the rice genome contains several genes that code for smaller sized (50-60 kD) alpha-amylases. All of the plant 50-60 kD alpha-amylases are similar in size to those from bacteria, yeast, and mammals that are used commercially. Activities of the 50-60 kD alpha-amylase enzymes from plants also are similar to those of bacterial, fungal, and mammalian alpha-amylase enzymes, in that they result in starch hydrolysis products consisting of maltose, maltotriose, or small oligosaccharides plus alpha limit dextrins. The activities of the 100 kD plant alpha-amylases and the nature of their starch hydrolysis products have not been characterized to date.

Alignment of the amino acid residues of all predicted alpha-amylases (both large and small) reveals they are highly similar in their C-terminal regions, which are believed to contain the catalytic domain of the protein [17]. The two 100 kD alpha-amylases from Arabidopsis and rice also have considerable amino acid sequence similarity, with 37% sequence identity in their N-terminal regions and 59% amino acid identity overall. The N-termini of the Arabidopsis and rice 100 kD alpha-amylases also have two small regions of similarity with another protein from Arabidopsis that has been termed the R1-protein, the product of the sex1 gene [26, 35]. Mutations in the sex1 gene result in excess starch accumulation, suggesting that a functional R1-protein is required for starch degradation. This suggests the larger 100 kD alpha-amylases from plants comprise a distinct isoform class of alpha-amylase enzymes. Further investigation into the role of the large alpha-amylase in starch metabolism, particularly in an agronomically important plant such as maize, is desirable.

BRIEF SUMMARY OF THE INVENTION

The invention is based on the discovery of a novel starch hydrolytic activity (called Starch Hydrolytic Enzyme, or SHE) in developing maize kernels. The specificity of native, purified SHE is similar, in general terms, to previously known alpha-amylases since both activities are able to hydrolyze starch, amylopectin, amylose, and beta-limit dextrin but are not able to hydrolyze the branched polymer pullulan. However, the activity of SHE toward amylopectin results in hydrolysis products that are distinctly different from those of other alpha-amylases. Specifically, they are of the same approximate molecular mass as beta-limit dextrins and do not include maltose or malto-oligosaccharides. This unique activity suggests that the novel maize alpha-amylase is an endo-hydrolytic enzyme that specifically cleaves long amylopectin chains (B₂ or B₃ chains) that extend between unit clusters in the molecule. In contrast, conventional maize amylases, in addition, clip off the smaller side chains of amylopectin. The new enzyme according to the invention, SHE, and its homologous equivalents in other plants such as rice, Arabidopsis, apple and potato, will have value in starch processing for generating different, and perhaps larger sized, alpha-limit dextrins for industrial use, as compared to those generated by previously known alpha-amylases or other starch hydrolytic enzymes. In addition, modification of the expression of this enzyme in transgenic maize plants or in other transgenic organisms (including bacteria, yeast, and other plant species) can be useful for the generation of novel starch forms or altered starch metabolism.

The cDNA encoding the new enzyme according to the invention, SHE, has also been isolated and sequenced. cDNA sequences encoding SHE or portions thereof can be incorporated into replicable expression vectors and the vectors transfected into an appropriate host (e.g., bacterial, yeast, eucaryotic cell culture). Alternatively, genomic DNA fragments encoding SHE can be utilized in situ. The SHE protein, in either naturally occurring or recombinant form, can be used in the starch processing industry or in other industries that employ starch for any purpose. The protein, or fragments thereof, also can be employed as an immunogen in order to raise antibodies against SHE.

Thus, the invention generally features a Starch Hydrolytic Enzyme, SHE, or portions thereof; nucleic acid isolates encoding SHE or portions thereof; methods of producing SHE or portions thereof; cells transformed with a recombinant vector containing a SHE-encoding alpha-amylase3 (Amy3) gene; antibodies to SHE or fragments thereof and methods to produce such antibodies; transgenic plants containing a SHE gene and methods to produce such transgenic plants; and methods of using a protein having SHE hydrolytic activity for starch degradation.

The invention also features a nucleic acid isolate able to hybridize under stringent conditions to the complement of a nucleic acid sequence encoding SHE, and the protein or polypeptide fragment, e.g., immunogenic fragment, thereof encoded by the nucleic acid isolate. The invention, furthermore, features a recombinant expression vector comprising a nucleic acid isolate able to hybridize under stringent conditions to the complement of a sequence encoding SHE, cells transformed with the recombinant expression vector, and methods of expressing the SHE protein or polypeptide fragment encoded within the recombinant expression vector.

Also featured is a method of producing the SHE protein, or polypeptide fragment thereof, comprising transforming a host cell with a nucleic acid able to hybridize under stringent conditions to a nucleic acid sequence encoding the SHE protein and linked to a nucleic acid sequence under the control of an inducible promotor, and inducing the cell to produce a fusion protein comprising the SHE protein, or polypeptide fragment thereof. The invention also features a SHE fusion protein, methods of producing antibodies to a SHE fusion protein and antibodies produced by such method.

As used herein, the terms “isolated” or “purified” refer to a nucleic acid or protein sequence that has been separated or isolated from the environment in which it was prepared or in which it naturally occurs. Such nucleic acid or protein sequences may be in the form of chimeric hybrids or fusions, useful for combining the function of the nucleic acid or protein sequences of the invention with other species and also include recombinant forms. The term “determinant” as used herein includes the site on an antigen at which a given antibody molecule binds. The term “immunogenic fragment” refers to a fragment of SHE protein that reacts with antibodies specific for a determinant of SHE.

The SHE protein can be used as an alternative hydrolase, along with bacterial and fungal starch hydrolases and debranching enzymes, for industrial starch processing applications. SHE-encoding cDNA (Amy3), SHE-encoding genomic DNA (Amy3), or portions thereof may be utilized as markers for the identification of specific corn varieties, and for the development of corn varieties with starch properties tailored for specific industrial applications. Amy3 cDNA or genomic DNA fragments can be used to produce these proteins or peptide fragments or as probes to identify nucleic acid molecules encoding related proteins or polypeptides (e.g., homologous polypeptides from related species and heterologous molecules from the same species). Assays for SHE function, production or expression by cells are made possible by the development of antibodies reactive with the SHE protein.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof and from the claims, taken in conjunction with the accompanying drawings in which:

FIG. 1 is a gel showing two-dimensional separation of starch-metabolizing enzymes from developing maize endosperm;

FIG. 2 is a flow chart showing a purification scheme for purifying the Starch Hydrolytic Enzyme (SHE) according to the invention;

FIG. 3 is a gel analysis of hydrolysis results showing the specificity of SHE toward different polysaccharides;

FIGS. 4A and 4B are graphs showing FACE analysis of hydrolysis products of amylopectin incubated with SHE (FIG. 4A) and a conventional alpha-amylase (FIG. 4B);

FIG. 5 is a graph showing GPG analysis (Sepharose CL-2B column) of the hydrolysis products of amylopectin incubated with purified SHE;

FIG. 6 is a graph showing GPG analysis (Sepharose CL-2B column) of the hydrolysis products of beta-limit dextrin incubated with purified SHE, overlaid on the graph of FIG. 5;

FIG. 7A is a graph showing GPC determination (Superose 6 column) of the molecular weight of SHE under native conditions;

FIG. 7B is a gel showing a molecular weight determination of SHE under denaturing conditions by SDS-PAGE 7% analysis;

FIG. 8 is a chart showing the results of MALDI-TOF analysis of tryptic peptides produced from digestion of the 94 kD form of SHE;

FIGS. 9A and 9B show the nucleotide sequence of ZmAmy3 cDNA (SEQ ID NO: 1) aligned with the amino acid sequence (single letter code) of the encoded SHE protein (SEQ ID NO: 2), according to the invention;

FIGS. 10A and 10B show a sequence alignment of the SHE protein according to the invention (SEQ ID NO: 2) with the predicted polypeptide sequences for both the rice (SEQ ID NO: 15) and the Arabidopsis 100 kD alpha-amylases (AMY3) (SEQ ID NO: 16); and

FIG. 11 shows a hypothetical reaction mechanism for SHE activity.

DETAILED DESCRIPTION OF THE INVENTION

Two-dimensional native PAGE/activity gel analysis (i.e., starch zymogram analysis) of proteins from developing maize kernels harvested 20 days after pollination (DAP) was used to identify a novel maize starch hydrolytic activity. As shown in FIG. 1, proteins in specific anion exchange chromatography fractions were separated by electrophoresis through a native polyacrylamide gel and then transferred to another polyacrylamide gel containing starch. Enzymatic activity that altered the starch substrate in the gel was visualized by staining with iodine solution. A distinct white activity band indicating starch hydrolysis, and not correlated with the activity of known starch hydrolytic enzymes, was identified in chromatography fractions 19-23.

This newly identified enzymatic activity was specifically isolated in a series of purification steps, including ammonium sulfate precipitation, anion exchange chromatography, gel permeation chromatography and affinity electrophoresis, as diagramed in FIG. 2. These purification steps resulted in a preparation of the enzyme that was devoid of other starch metabolizing activities. Those fractions containing purified SHE activity were pooled and used to carry out various incubation experiments with different polysaccharide substrates.

The glucan substrate specificity of this novel enzyme, called here Starch Hydrolytic Enzyme (SHE), was determined by zymogram analysis. As shown in FIG. 3, the specificity of SHE is similar, in general terms, to that of previously known alpha-amylases. Both activities are able to hydrolyze starch (Sta), amylopectin (Ap), amylose (Am) and the beta-limit dextrin of amylopectin (β-LD), but they are not able to hydrolyze the branched isomaltotriose polymer called pullulan (Pul).

Differences between SHE activity and that of conventional alpha-amylases were detected, however, after extended incubation of the purified SHE protein with starch, amylopectin, and beta-limit dextrin. Each individual substrate was incubated overnight with SHE or with a lower molecular weight alpha-amylase similarly purified from the same maize endosperm tissue (a “conventional” alpha-amylase). The hydrolysis products were analyzed by fluorophore-assisted capillary electrophoresis (FACE) [7, 25]. As indicated in FIG. 4A, SHE activity does not release small oligosaccharides (i.e., short chains consisting of 1 to 8 units of glucose), in contrast to the activity of the conventional maize alpha-amylase (FIG. 4B).

The hydrolysis products were further characterized by gel permeation chromatography on a Sepharose CL-2B column. FIG. 5 displays the analysis of hydrolysis products that resulted from the incubation of amylopectin with purified SHE. In addition, FIG. 6 compares the analysis of FIG. 5 with that of hydrolysis products resulting from the incubation of beta-limit dextrin with SHE. These experiments demonstrate that purified SHE activity hydrolyzes both branched polysaccharides, as indicated by significant decreases in the molecular mass of each. However, the results also indicate that the hydrolysis products themselves are of high molecular weight, because no short glucosyl chains were detected by the FACE analysis (see FIG. 4).

The apparent molecular weight of SHE was determined by gel permeation chromatography following passage of the purified protein over a Superose-6 column. Comparison of the migration of the activity to that of known molecular weight standards provided the estimate that SHE is approximately 366 kD (FIG. 7A). However, analysis of purified SHE under denaturing conditions by SDS-PAGE, followed by staining with Coomassie-Blue (FIG. 7B), revealed that the molecular weight of the SHE polypeptide monomer is approximately 94 kD. This suggests that the purified SHE activity results from the formation of an enzyme complex that most likely is comprised of four SHE subunits.

The identity of the purified protein shown in FIG. 7B was established by subjecting the 94 kD polypeptide to mass spectrometric analysis (MALDI-TOF) following trypsin digestion. The mass of each tryptic peptide was determined, and these were compared to the masses of tryptic peptides of all known proteins available in the databases. Database analysis determined that the protein identity is closest to that of the 100 kD alpha-amylase that is the predicted product of the rice large alpha-amylase gene (AMY3) (Genbank AP003408) (FIG. 8).

Based on the results of the mass spectrophotometric analysis, the rice Amy3 gene sequence was used to search the Maize Gene Database for similar sequences. This database contains a partial sequence of the maize genome, including “expressed sequence tags” (ESTs) representing partial gene sequences. The database search uncovered a partial maize polypeptide sequence predicted from a 548 nt EST sequence (Genbank PCO139185) that closely matches the predicted polypeptide sequences for both the rice and the Arabidopsis 100 kD alpha-amylases (At1g69830), as shown in FIG. 10.

The full-length coding sequence for the maize Amy3 (ZmAmy3) cDNA was PCR amplified using gene-specific primers complementary to the 3′ end of the maize EST and degenerate primers based on the 5′ region of the rice Amy3 gene sequence. The 2640 bp ZmAmy3 cDNA product (FIGS. 9A and 9B, SEQ ID NO.:1) is predicted to code for a polypeptide of approximately 99 kDa (SHE) (FIGS. 9A and 9B, SEQ ID NO.:2). At the amino acid level, the maize and rice sequences are 97% identical over the length of the polypeptide fragment predicted from the maize EST, and at the nucleic acid level the maize and rice sequences are 86% identical for this region. This high degree of sequence identity indicates that the maize EST derives from the maize Amy3 gene and that the purified SHE protein and the predicted rice AMY3 protein are homologous.

Comparisons of the deduced, full-length SHE amino acid sequence with the corresponding AMY3 sequences from rice and Arabidopsis revealed that all three large alpha-amylase polypeptides are closely conserved. Overall, the maize SHE sequence has 79% identity with the rice AMY3 polypeptide and 62% identity with the Arabidopsis AMY3 polypeptide. The rice and Arabidopsis AMY3 amino acid sequences are 59% identical. In the N-terminal regions, the rice and maize AMY3 polypeptides are 60% identical. Because the three known AMY3 polypeptides (including maize SHE) also have high sequence similarity to 50-60 kD AMY1 and AMY2 sequences from rice, Arabidopsis, and maize at their C-termini, they represent divergent plant alpha-amylase isoforms. The enzymatic activity of this class of alpha-amylase isoforms (AMY3) has not been characterized to date.

Use

The starch hydrolytic activity from maize kernels (SHE) described herein exhibits a novel alpha-amylase activity. As indicated above, the activity of this enzyme toward amylopectin results in hydrolysis products that are of the same approximate molecular mass as beta-limit dextrins. However, SHE activity does not result in the production of maltose or malto-oligosaccharides, as would be expected from any known, conventional alpha-amylase. This unique activity suggests that SHE is an endo-hydrolytic enzyme that specifically cleaves long amylopectin chains (B₂ or B₃ chains) that extend between unit clusters in the molecule, thus generating larger sized alpha-limit dextrins.

Referring to FIG. 11, a typical branched glucan substrate such as amylopectin 10, in which branch chains are arranged in distinct clusters 12, 14 connected by single (non-branched) B₂ or B₃ chains 16, would be acted upon differently by SHE and a conventional alpha-amylase. According to this model, SHE, by virtue of its assembly state and size (a 366 kD tetramer 18), would be barred from access (pathway 20) to the glucan chains in the interior regions of amylopectin, clusters 12, 14. Thus, SHE hydrolysis would be limited only to those regions of the amylopectin molecule that are accessible to the enzyme, for example the long linear chains 16 that extend between individual cluster units. No other enzyme is known that cleaves starch specifically in regions external to the unit clusters, producing larger sized alpha-limit dextrins 26. This is in stark contrast to the action (pathway 22) of conventional, smaller sized alpha-amylases, which function as monomers 24 and are likely to penetrate all regions of the amylopectin molecule, producing a mixture of small oligosaccharides and larger products 28.

Use of the ZmAmy3 cDNA that encodes SHE will make possible the isolation of active portions of SHE protein and, thus, the development of highly active, recombinant enzyme preparations for starch processing. In addition, ZmAmy3 cDNA can be used to isolate the cDNA encoding the homologous AMY3 enzymes from other plants with important starch hydrolytic pathways, such as rice, Arabidopsis, apple and potato.

As indicated above, recombinant SHE and/or the native maize enzyme, recombinant AMY3 enzymes from other plant species and active fragments thereof will have value in starch processing for consistently generating different, larger sized alpha-limit dextrins (maltodextrins) for industrial use. In comparison, the previously known alpha-amylases could be used to generate larger sized alpha-limit dextrins only by manipulating enzyme concentrations and/or incubation times, reaction conditions that could not be counted on to consistently produce the same products from batch to batch.

These new maltodextrin products will have value in food production as thickeners, emulsifiers, ice crystal retardants, texturizing agents, and/or fat or oil substitutes [13]. In manufacturing and pharmaceutical industries, the new maltodextrin products of SHE hydrolysis will have value as coating or encapsulation agents (e.g., for tablets or drug delivery), or as adhesive or binding agents.

The new enzyme according to the invention, SHE, and its homologous equivalents also will have value for the production of high MW dextrins that can potentially be used for the manufacture of biopolymers. Native and destructured starches have long been employed as particulate fillers and in commodity plastics [33]. Biopolymer blends containing either chemically modified or native starch forms are continually being examined for their effectiveness as packaging materials and biomedical adhesive agents [8, 22]. Large maltodextrins, such as those produced by SHE, may confer altered tensile properties and reduced water sensitivity to biopolymer blends.

Furthermore, the new enzyme according to the invention, SHE, and its homologous equivalents will have value as unique enzymes that can be added to formulations designed to selectively degrade starch. In addition, modification of the expression of the SHE enzyme and/or its homologous forms in transgenic maize plants or in other transgenic organisms (including bacteria, yeast, and other plant species) can be useful for the generation of novel starch forms or altered starch metabolism.

Experimental Procedures Maize Stocks and Allele Nomenclature

Wild type maize inbred lines in the W64A or the Oh43 inbred genetic backgrounds are used for analysis. Kernels are harvested 19-21 days after pollination (DAP), quick frozen in liquid nitrogen, and stored at −80° C. Prior to protein extraction, endosperm tissue is separated from embryo and pericarp tissues.

The nomenclature follows the standard maize (Zea mays L.) genetics format [1]. Names and symbols of genetic loci are italicized. Messenger RNAs and cDNAs are designated by italic font with the first letter capitalized, whereas polypeptide symbols are not italicized and are in upper case letters. Species designations for orthologous loci are distinguished by having the first letter of both the genus and the species precede the locus designation (e.g., ZmAmy3 designates the Zea mays Amy3 cDNA).

Protein Extraction and Activity Gel Analysis

Protein isolation from endosperm is as described [7]. Briefly, frozen kernels (5 g) are ground to a fine powder in liquid nitrogen with a mortar and pestle, and the tissue is suspended in 5 mL of buffer containing 50 mM sodium acetate, pH 6, and 20 mM DTT. All of the lysates are centrifuged at 50,000 g for one hour at 4° C. Protein concentrations are determined according to the method of Bradford [3, 4].

For one-dimensional native PAGE activity gel analysis (i.e., zymogram analysis), total proteins (approximately 100 μg) are separated on a native polyacrylamide gel (16 cm×20 cm×0.15 cm). The resolving gel contains 7% (w/v) acrylamide (29:1 acrylamide-bisacrylamide [Sigma]) and 375 mM Tris-HCl, pH 8.8. The stacking gel contains 4% (w/v) acrylamide and 63 mM Tris-HCl, pH 6.8. Electrophoresis is conducted at 4° C., 25 V cm⁻¹ for 4 h using a Protean II cell (Bio-Rad) in an electrode buffer of 25 mM Tris, 192 mM glycine, pH 8.8, and 2 mM DTT. At the end of the run, the gel is electroblotted to a polacrylamide gel of the same size containing 76 acrylamide, 0.3% (w/v) potato starch (Sigma), and 375 mM Tris-HCl, pH 8.8. Alternative substrates to starch in the transfer gel include 0.3% (w/v) amylopectin (Sigma), 0.3% (w/v) amylose (Sigma), 0.36 (w/v) beta limit-dextrin (Megazyme), 0.36 (w/v) oyster glycogen (Sigma), and 0.3% (w/v) azure pullulan (Sigma). The transfer is performed overnight at 20 V in the electrode buffer at room temperature. Starch metabolic activities are observed by staining the gel with I₂/KI solution, and the gel is photographed immediately.

For two-dimensional zymogram analysis, total proteins (40 μg) are extracted as described above and loaded onto an anion exchange chromatography (MonoQ HR 5/5) using AKTA FPLC instrumentation (Amersham-Pharmacia). The MonoQ column is equilibrated with buffer A (50 mM Tris-acetate, pH 7.5; 10 mM DTT). Bound proteins are eluted with a 48 mL-linear gradient of 0 to 500 mM NaCl in buffer A containing 1M NaCl. The flow rate is 0.9 mL/min, and 1 mL fractions are collected. Proteins in each fraction are separated by non-denaturing PAGE. Following electrophoresis, proteins are transferred by electroblotting to a polyacrylamide gel of the same size containing 0.3% (w/v) starch. Starch metabolic activities are observed after staining the gel with I₂/KI solution, as described [7]. Transfer is performed overnight as described for the one-dimensional zymogram.

Protein Purification

The unknown glucan hydrolytic activity (termed “SHE”) detected by one- and two-dimensional native PAGE activity gel analysis was purified in a step-wise manner from crude protein extracts isolated from approximately 100 grams mid-development maize kernels. At the conclusion of each purification step, starch zymogram analysis was employed to identify the fraction(s) containing SHE activity. The first step in the purification scheme was fractionation by ammonium sulfate precipitation, in which proteins were precipitated by the slow addition of saturated ammonium sulfate to 40% saturation. After incubation at 0° C. for 30 min, proteins were collected by centrifugation at 20,000 g for 20 min. The protein pellet was dissolved in 5 mL Buffer A and dialyzed twice against 400 mL Buffer A, according to previously described methods [5].

Dialyzed proteins were injected onto a FPLC MonoQ HR 5/5 column using AKTA FPLC instrumentation (Amersham-Pharmacia), preincubated with Buffer A. Bound proteins were eluted with a 48 mL-linear gradient of 0 to 500 mM NaCl in buffer A containing 1M NaCl. The flow rate was 0.9 mL/min, and 1 mL fractions were collected. MonoQ fractions containing SHE activity were pooled and further purified by gel filtration chromatography (GPC) on a Sephacryl S400 column (Amersham-Pharmacia). GPC was performed at 4° C. in buffer A at a flow rate of 0.4 mL/min, and 1 mL fractions were collected. Fractions containing SHE activity were pooled and concentrated using an Amicon centricon microspin column (Millipore) to 500 μL. A second GPC purification was performed by application of 100 μL of the concentrated SHE-containing sample to a Superose 6 column (Amersham-Pharmacia). Superose 6 GPC was at 4° C. in buffer A with a flow rate of 0.2 mL/min, and 0.3 mL fractions were collected. Identification of the Superose 6 fractions containing SHE activity was achieved by starch zymogram analysis, which also provided the final step in the purification process, determination of the affinity of the purified protein for the starch substrate in the gel.

Purification of “conventional” alpha amylase from maize was achieved by the same methods as described for the purification of SHE. In this case, the alpha amylase activity was monitored at each step in the purification process enzymatically, using the Ceralpha kit (Megazyme). Briefly, this method assays the production of p-nitrophenol at 410 nm, which results from the hydrolysis of non-reducing ends that are blocked with p-nitrophenyl maltoheptaoside. Assays for “conventional” alpha amylase activity were conducted at 30° C. for 30 min and were terminated by the addition of 1% (w/v) Trizma base (Sigma).

Characterization of Purified Protein

The approximate molecular mass of SHE was determined by comparison of the elution of SHE from the analytical Superose 6 column to the elution of known MW standards from same column. Standard proteins used to calibrate the column were bovine thyroglobulin (670,000), bovine gamma globulin (158,000), chicken ovalbumin (44,000), horse myoglobin (17,000) and vitamin B-12 (1,350) (Bio-Rad).

Protein in pooled, concentrated Superose 6 fractions containing SHE activity was analyzed by SDS-PAGE on a 7% polyacrylamide gel, followed by staining of the gel with Coomassie brilliant blue and destaining with 50% methanol solution, according to standard procedures [29]. The approximate molecular mass of the strongly stained, abundant polypeptide corresponding to SHE was determined by comparison of the migration distance of the polypeptide with the migration of commercial molecular weight standards (Bio-Rad).

To identify the SHE protein in terms of its amino acid sequence, the band corresponding to SHE was excised from the SDS-polyacrylamide gel and analyzed by time-of-flight mass spectrometry (MALDI-TOF) according to standard methods [21]. At the mass spectrometry facility (Protein Facility, Iowa State University), the polypeptide was digested with the protease trypsin. The peptide fragments were concentrated, fractionated by capillary electrophoresis, and the eluent from the capillary was directly injected into the electrospray mass spectrometer, which separated the individual peptides. Computational algorithms utilized the differences between fragment masses to reveal the amino acid sequence of the original peptide, based on the expectation of fragmentation by cleavage of the peptide bonds. The peptide sequences were then compared to proteins in the public databases, enabling the sequence match of a peptide in a given gel band to a peptide within a protein sequence in the database.

Characterization of Hydrolysis Products

Purified SHE activity was analyzed by incubation of 20 μL of the pooled and concentrated Superose 6 fractions containing SHE activity with 100 μL of a 1% amylopectin (Sigma) or 1% beta limit-dextrin (Megazyme) solution in a total volume of 200 μL. Incubation was at 37° C. for 24 h. Control incubations with both substrates also were conducted using “conventional”, maize alpha amylase purified from developing maize endosperm, under the same conditions described for SHE incubation. Equivalent amounts of SHE and the alpha amylase control proteins were determined by quantification of the protein sample according to standard methods [3].

SHE amylopectin hydrolysis products were analyzed using a modified protocol for fluorophore-assisted carbohydrate electrophoresis (FACE) [7, 25]. Briefly, a 10 μL aliquot of the SHE amylopectin hydrolysis products was lyophilized, then resuspended in 30% DMSO and boiled for 10 min. A 10 μL aliquot was diluted to a final volume of 50 μL with 50 mM sodium acetate, pH 4.5. Pseudomonas sp. isoamylase (1 μL, 0.3 units) (Catalog No. E-ISAMY, Megazyme International, Bray, Ireland) was added and the reaction incubated overnight at 42° C. The mixture was heated in boiling water for 5 min and then centrifuged for 2 min at 12,000 g. A 10 μL sample of the reaction was evaporated to dryness in a Speed Vac. The reducing ends of the liberated oligosaccharide chains were derivatized with the fluorescent compound 8-amino-1,3,6-pyrenetrisulfonic acid (APTS) (Catalog No. 09341, Sigma-Aldrich, St. Louis, Mo.) by suspending the dried sample in 2 μL of 1 M sodium cyanoborohydride in tetrahydrafuran (Catalog No. 29, 681-3, Sigma-Aldrich) and 2 μL APTS (0.1 mg/μL in 15% acetic acid). The reaction was incubated overnight at 42° C., diluted with 46 μL water, vortexed, and centrifuged briefly in a microfuge. A 5 μL aliquot was added to 195 μL purified water, and this sample was applied to a Beckman P/ACE capillary electrophoresis instrument. The sample injection parameters were 5 s at 0.5 psi. Separation was accomplished at 23.5 kV in an uncoated capillary using Carbohydrate Separation Gel Buffer N (Catalog Nos. 338451 and 477623, respectively, Beckman Coulter, Inc., Fullerton, Calif.).

SHE amylopectin and beta-limit dextrin hydrolysis products also were analyzed by GPC, using a Sephacryl CL-2B column (Amersham-Pharmacia; Ø32 18 cm; H=50 cm) equilibrated with 10 mM NaOH. A 100 μL volume of the hydrolysis product was applied to the CL-2B column, and eluted at a flow rate of 12 mL/h in 1.4 mL fractions. Aliquots (30 μL) of each fraction were incubated with 50 μL amyloglucosidase solution (0.3 U in a 50 mM sodium citrate buffer, pH 4.6; Megazyme). The μg of glucose equivalents in each fraction was determined by the colorimetric glucose oxidase/peroxidase method (Sigma Diagnostics).

PCR Amplification, Cloning of ZmAmy3 cDNA and Nucleotide Sequence Analysis of the ZmAmy3 cDNA

Total RNA was isolated from approximately 10 g Zea mays kernels (Oh43 inbred background) harvested 19 days after pollination, using a modification of the protocol reported by Chomczynski and Sacchi [6]. Briefly, frozen kernels were ground to a powder in liquid nitrogen, and RNA was extracted with Trizol reagent (Invitrogen). Addition of chloroform separated polysaccharides and DNA from the RNA-containing aqueous fraction. The RNA was then precipitated and air-dried, resuspended in water, and treated with DNase. The RNA was further purified using an RNeasy Plant Mini Kit (Qiagen).

Approximately 5 μg total RNA from developing maize kernels was reverse transcribed (RT) using a Superscript III First-Strand Synthesis System for RT-PCR kit (Invitrogen), using the oligo-(dT)18 primer provided. The RT product was used as the template for PCR amplification of a 2451 bp fragment of the ZmAmy3 cDNA. Five ZmAmy3 gene-specific primers were designed based on the sequence of an EST fragment in the maize genome (Genbank accession number PCO139185). These primers are designated KS052 (5′-GCC AAG TCT ATG AAG ACG CTT CC-3′) (SEQ ID NO: 3), KS055 (5′-GCT GAT GGA GCA GGA AAC TC-3′) (SEQ ID NO: 4), KS056 (5′-CTT CAG GCG ACA CAG AAT CA-3′) (SEQ ID NO: 5), KS057 (5′-CTA CAA TCA GGA TGC CCA CA-3′) (SEQ ID NO: 6), and KS058 (5′-AAC AAA GTT GAC AGC GGC GAT TGG A-3′) (SEQ ID NO: 7). Degenerate primers were designed based on predicted orthologous sequences of the Arabidopsis thalianai Amy3 gene (Genbank accession number BT000643) and Oryza sativa Amy3 gene (Genbank accession number NM_(—)191752). The degenerate primers are KS047 (5′-GGV AAR TGG GTS TTR CAT TGG GG-3′) (SEQ ID NO: 8) and KS048 (5′-GGV AAR TGG GTS CTS CAT TGG GG-3′) (SEQ ID NO: 9) (V=A, C or G; R=A or G; S=G or C). PCR amplification was conducted according to the protocol specified by the Accuzyme Pfx PCR Amplification kit (Invitrogen), using 500 μg of the template DNA, and equivalent amounts (0.5 ρmol, final concentration) of primers KS052, KS047, and KS048. The complete nucleotide sequence of both strands of the amplified fragment was obtained using the three PCR primers as well as primers KS055, KS056, and KS057.

To obtain the 5′ end of the ZmAmy3 cDNA, the rapid amplification of cDNA ends (RACE) [10] protocol was employed, using the GeneRacer kit (Invitrogen), according to instructions provided with the kit. Briefly, 5 μg RNA from maize kernels was reverse transcribed using the ZmAmy3-specific primer KS052 (0.5 μmol, final concentration). PCR amplification of the 5′ end was performed with Accuzyme Pfx polymerase, according to the kit protocol, using primer KS052 and a primer provided by the GeneRacer kit (5′-CGA CTG GAG CAC GAG GAC ACT GA-3′) (SEQ ID NO: 10). The amplified DNA fragments were gel purified using the Qiaquick Gel Extraction kit (Qiagen). The purified PCR product was used as the template for a second-round PCR reaction using a nested ZmAmy3-specific primer KS059 (5′-GGG CTG TCC TTC TGA ATT GGG CAA A-3′) (SEQ ID NO: 11) and a nested GeneRacer primer (5′-GGA CAC TGA CAT GGA CTG AAG GAG TA-3′) (SEQ ID NO: 12). The amplified products were gel purified and sequenced using the same primers that were used for the amplification.

The PCR fragment containing the amplified ZmAmy3 cDNA was re-amplified for the purpose of cloning the fragment into a plasmid vector. Following a protocol based on the recombination-mediated cloning strategy of the Gateway Technology system (Invitrogen), two new PCR primers were used for the amplification: KS062 (5′-GGG GAC AAG TTT GTA CAA AAA AGC AGG CTG GGA AGT GGG TAC TGC ACT GGG G-3′) (SEQ ID NO: 13), and KS063 (5′-GGG GAC CAC TTT GTA CAA GAA AGC TGG GTG CCA AGT CTA TGA AGA CGC TTC C-3′) (SEQ ID NO: 14). The PCR product was gel purified and cloned into the Gateway cloning vector pDONR221 using the Invitrogen BP Clonase Enzyme Mix, according to the recommended protocol, generating plasmid pKS024. E. coli cells (DH-5α) were transformed with the plasmid DNA and screened for successful transformation events on LB media containing kanamycin. Plasmid DNA was isolated from successful transformants and the identity of pKS024 is confirmed by restriction enzyme analysis. Plasmid DNA was digested with both ApaI and HindIII, which produces fragments of 3738 and 1114 bp; BamHI, which produces fragments of 4449 and 553 bp; and with EcoRV and produces fragments of 2903 and 2100 bp.

The nucleotide sequence of plasmid pKS024 was determined by the chain termination method [30] using Sequenase Version 2.0 (U.S. Biochemical Corp.). The plasmid has been deposited with the American Type Culture Collection.

Deposits

Plasmid pKS024 was deposited on Sep. 24, 2004, with the American Type Culture Collection (ATCC), P.O. Box 1549, Manassas, Va. 20108 USA, as ATCC No. PTA-6235.

Applicants' assignee, Iowa State University Research Foundation, represents that the ATCC is a depository affording permanence of the deposit and ready accessibility thereto by the public if a patent is granted. All restrictions on the availability to the public of the material so deposited will be irrevocably removed upon the granting of a patent. The material will be available during the pendency of the patent application to one determined by the Commissioner to be entitled thereto under 37 CFR 1.14 and 35 USC 122. The deposited material will be maintained with all the care necessary to keep it viable and uncontaminated for a period of at least five years after the most recent request for the furnishing of a sample of the deposited microorganism, and in any case, for a period of at least thirty (30) years after the date of deposit or for the enforceable life of the patent, whichever period is longer. Applicants' assignee acknowledges its duty to replace the deposit should the depository be unable to furnish a sample when requested due to the condition of the deposit.

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While the present invention has been described in conjunction with a preferred embodiment, one of ordinary skill, after reading the foregoing specification, will be able to effect various changes, substitutions of equivalents, and other alterations to the compositions and methods set forth herein. It is therefore intended that the protection granted by Letters Patent hereon be limited only by the definitions contained in the appended claims and equivalents thereof. 

19. A method of processing starch comprising the steps of: providing a sample of starch to be processed; and treating said sample of starch with an enzyme preparation comprising a protein, or polypeptide fragment thereof, encoded by a nucleic acid isolate able to hybridize under stringent conditions to the complement of a nucleic acid sequence encoding the SHE protein having the amino acid sequence shown in FIGS. 9A and 9B (SEQ ID NO:2). 